This Review discusses the complex role of the gut microbe Akkermansia muciniphila in human health.

Gut microorganisms capable of producing ethanol cause alcohol intoxication, which can be corrected via faecal microbiota transplantation.

A short peptide derived from a commensal-fungal-secreted protein promotes repair in models of colon epithelial damage when delivered directly or via probiotic microbes.

Vaginal birth, exclusive breastfeeding and early contact with siblings promote colonization of the infant gut with bifidobacteria capable of producing aromatic lactates, a microbial and metabolite signal that is inversely related to the risk of allergen-specific sensitization and dermatitis later in life.

Large-scale computational and in vitro analyses identify commensal type III secretion systems and substrates in the human gut microbiome that can interact with human proteins to modulate immune pathways.

Without key cell cycle control genes, SAR11 cells experience aneuploidy and growth inhibition when exposed to changes in nutrients, carbon sources or temperature stress, a vulnerability that may represent an evolutionary trade-off for adaptation to oligotrophic environments.

Limiting phosphate concentrations could be a strategy to protect and sequester carbon dioxide as fucoidan, a polysaccharide produced by marine algae.

An alternative mating system, termed parasex, produces progeny with high levels of genotypic diversity and is able to fulfil the roles of meiosis when it is absent in the fungal pathobiont Candida albicans.

Whole-genome sequencing of polioviruses in Uganda following nOPV2 use showed high genetic stability and no sustained transmission, even though a rare double recombinant strain regained virulence, but did not spread due to high vaccination coverage.

A library of 400 phage protein-coding genes is used to find a trove of antiphage systems, revealing systems that target tail fibre and major capsid proteins.

Jacob Smith interviews microbiologists from around the world for their insights about what’s next for the field. Despite numerous challenges, optimism and creativity are poised to usher in an exciting new era of microbiology.

Our January 2026 special issue commemorates the tenth anniversary of the journal and celebrates researchers, peer reviewers and readers from the microbiology community and beyond.

For the celebration of our tenth anniversary, Nature Microbiology asks the former editors to reflect on their time at the journal.

Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways.

A new community-led checklist provides reporting guidelines for microbiome research across environments.